User Manual - Duke University
Contents
1. resFormat Format of resonance assignments It can be CYANA format BMRB format or KEASY format resNameScheme Atom naming scheme It can be BMRB OLD BMRB NEW PDB NEW or PDB OLD resonance File name of resonance assignment list NOESY Format Format of NOESY cross peak list It can be XEASY format or NMRVIEW format 3D N15 NOESY File name of 3D 15N labeled NOESY cross peak list 3D C13 NOESY File name of 3D 13C labeled NOESY cross peak list isUnique Whether only those unique NOE assignments are outputted or all ambiguous NOE assignments are outputted isOutORFormat Whether multiple NOE assignments assigned to the same NOESY cross peak are outputted in OR format outNoeName File name of the output NOE table which is in the standard Xplor format The default atom name scheme used in the output NOE assignment table is PDB NEW CompareTwoNOETables CompareTwoNOETables input This command compares two NOE table and outputs the summary A typical input parameter file includes the following parameters Sequence File name of protein primary sequence NOEFormat Format of source NOE table It can be XPLOR format or CYANA format NOE Table File name of source NOE table for comparison RefNOEFormat Format of reference NOE table It can be XPLOR format or CYANA format Ref NOE Table File name of reference NOE table for comparison2. IsOne20ne whether it is one to one packing or one to all packing namely packing one structure to all structure in an ensemble It is set to be 1 for one to one packing 0 for one to all packing SSES PDB names of two SSE fragments which are separated by outPackedStructures File name of the output packed structures only the common name of all structures in the ensemble NOE Table File name of NOE restraint table used for packing SSEs NOEFormat Format of NOE restraint table It can be XPLOR or CYANA format isSkipSymCheck Whether the symmetry checking step is inputted It can be 1 or 0 SymID Assigned symmetry ID i e 0 1 2 3 if previous isSkipSymCheck is set to be 1 isSkipOutEnsemble Whether the step of outputting the whole ensemble of packed is skipped If this step is skipped only the mean structure of all packed structures is outputted InputFileLocation Location of the input ensemble of SSE fragments in the all to one packing case addSideChains addSideChains input This commands places the side chains onto backbone using the NOE pattern matching technique A typical input parameter file includes the following parameters Sequence File name of protein primary sequence haErr hlErr cl3Err hnErr nErr Error windows in each dimension ppm resFormat Format of resonance assignments It can be CYANA format BMRB format or
3. BMRB OLD BMRB NEW PDB NEW or PDB OLD isWholeStructure Whether the whole structure i e including sidechains and backbone is used for pruning ambiguous NOEs It is set to be 1 if the original backbone PDB file is used for pruning ambiguous NOEs resFormat Format of resonance assignments It can be CYANA format BMRB format or KXEASY format resNameScheme Atom naming scheme It can be BMRB OLD BMRB NEW PDB NEW or PDB OLD resonance File name of resonance assignment list NOESY Format Format of NOESY cross peak list It can be XEASY format or NMRVIEW format 3D N15 NOESY File name of 3D 15N labeled NOESY cross peak list 3D C13 NOESY File name of 3D 13C labeled NOESY cross peak list noeLimit Distance upper limit used for pruning ambiguous NOE assignment The original distance bound calibrated if the value of noeLimit is negative isOutORFormat Whether multiple NOE assignments assigned to the same NOESY cross peak are outputted in OR format outNoeName File name of the output NOE table which is in the standard Xplor format The default atom name scheme used in the output NOE assignment table is PDB NEW IsOriginalUp In the output NOE table whether the original NOE upper bounds i e calibrated from NOESY peak intensity are displayed The calibrated distance is used if the parameter is set to be 1 If the parameter is 0 the distances from the st
4. See the GNU Lesser General Public License for more details Full licensing details including citation requirements for the various different modules of the software are found in the document license pdf enclosed with this package distribution RDC PANDA is specifically designed for automated NMR NOE assignment and protein structure determination package It provides a novel approach for computing the initial structure template for NOE assignment by exactly solving backbones from RDCs and systematically choosing rotamers based on NOE pattern matching RDC PANDA mainly consists of following three algorithmic modules 1 RDC ANALYTIC which computes orientations and conformations of SSE backbones Current version of RDC ANALYTIC is designed to compute protein global fold backbone using NH and CH RDCs in one alignment medium It determines the conformations and orientations of secondary structure elements SSEs by solving the RDC equations in closed form It applies a systematic search approach to compute the global optimal solution of each SSE fragment that best fits the RDC data The RDC ANALYTIC module has been implemented in a standalone package More details about configurations and input file formats of RDC ANALYTIC can be found in its user manual released with this package distribution 2 PACKER which packs SSE backbones using spare NOE restraints PACKER first extracts a set of sparse unambiguous NOE assignments using only chemical shift
5. KEASY format resNameScheme Atom naming scheme It can be BMRB OLD BMRB NEW PDB NEW or PDB OLD resonance File name of resonance assignment list NOESY Format Format of NOESY cross peak list It can be XEASY format or NMRVIEW format 3D N15 NOESY File name of 3D 15N labeled NOESY cross peak list 3D C13 NOESY File name of 3D 13C labeled NOESY cross peak list LocationBBEnsemble Location of backbone ensemble outStructureName Name of the output structure name including both backbones and side chains addRandomLoops addRandomLoops input This command simply merges the SSE PDB and loop PDB into a PDB that contains the whole structure It prepares the input PDB files to Xplor in the local minimization approach A typical input parameter file includes the following parameters LocationSSEEnsemble Location of the input SSE ensemble LoopPDBName File name of loop PDB outCompleteStructures File name of output structures HANA NOE Asg HANA NOE Asg input This command executes the HANA NOE assignment algorithm given the backbone solved from RDC EXACT A typical input parameter file includes the following parameters Sequence File name of protein primary sequence haErr hlErr cl3Err hnErr nErr Error windows in each dimension ppm Backbone PDB file name of the backbone PdbNameScheme Atom naming scheme of backbone PDB It can be
6. TE FE HE TE FE FE FE FE FE HE TE FE E TE FE HE EE EE ER ER EE E FE E EH AE E E E E E E E E E EE EE H Note For short loops we can directly obtain NOE assignments from the mean structures of the ensemble cd cd cp av xplor local min average all pdb xplor final cal extract the unique NOE assignments for long loops in residues 33 41 using only chemical shift information The result will be stored in xplor final cal ubiquitin noe loopsl O0 tbl java cp bin RdcPanda NOEAsgFromCS asg noe csl input LongLoopsNOEAsgl out extract the unique NOE assignments for long loops in residues 50 65 using only chemical shift information The result will be stored in xplor final cal ubiquitin noe loops2 O0 tbl java cp bin RdcPanda NOEAsgFromCS asg noe cs2 input LongLoopsNOEAsg2 0ut extract SSE fragments including short loops that is excluding two long loops java cp bin RdcPanda ReadPdbFragments readPdbFragments input readPdbFragments out java cp bin RdcPanda ReadPdbFragments readPdbFragments2 input readPdbFragments2 out fUse HANA to compute NOE assignments in SSE and short loop regions fThe result will be stored in xplor final cal ubiquitin noe sses tbl java cp bin RdcPanda HANA NOE Asg HANA NOE Asg SSE input gt DANA NOE ASG SSE out FEE AE E FE AE FE EFE AERE HE EH EH E iteration 1 for computing long loops in residues 33 41 and residues 50 65 cd SPWD xplor fin
7. ANDA 2 License Information The source header below must be included in any modification or extension of the source code of RDC PANDA Source Header RDC PANDA NOE Assignment and Protein Structure Determination Version 1 0 Copyright C 2001 2009 Bruce Donald Lab Duke University RDC PANDA is free software you can redistribute it and or modify it under the terms of the GNU Lesser General Public License as published by the Free Software Foundation either version 3 of the License or at your option any later version RDC PANDA is distributed in the hope that it will be useful but WITHOUT ANY WARRANTY without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE See the GNU Lesser General Public License for more details You should have received a copy of the GNU Lesser General Public License along with this library if not see http www gnu org licenses There are additional restrictions imposed on the use and distribution of this open source code including A this header must be included in any modification or extension of the code B you are required to cite our papers in any publications that use this code The citation for the various different modules of our software together with a complete list of requirements and restrictions are found in the document license pdf enclosed with this distribution Co
8. E ERE RE E E E E EE EH E E E EEE ERE 3 Use Packer to pack SSEs FE HE TE FE E TE FE FE HE FE FE HE FE FE HE TE FE HE TE FE E TE FE FE FE FE FE E HE EE EE EE EE HE HH HE EE E E E E E E E E E EE H After computing comformations and orientations of SSE bacbone fragments save the pdb of each SSE backbone fragment in the directory inputFiles Then run the following command for packing helix and beta sheet java cp bin RdcPanda SSEPacking packingSSEs input gt packingSSE out fThe ensemble of all packed structures will be stored in directory inputFiles packing HEHEHE TE FE FE HE EE EH EH EH HH HE TE FE HE HE EE HE EE EE EE EE HE HH E TE FE EE EE E E E E EE E H 4 Use HANA to place side chains HERE EEE EH EH EH EH EH HH FE E TE FE FE TE EE EERE ER ER E E EE EE EE E E HEE EE HE Run the following command line to place side chains onto all packed SSE backbone i e core structures java cp bin RdcPanda addSideChains addSideChains input gt addSideChains out The ensemble of outputted packed SSE backbones with computed side chains will be stored in directory inputFiles bbwsc HERE RHE HEHE RHEE EEE RHE HE EE FE FE HERE HE FE AE HEHE E FE E FE E FE HE HERE EEE H 5 Compute the loops FE HE AE FEAE FEAE FEAE FEAE FEAE FEE HE FE HEFE FE FE RHE HERE FE FE E HERE AE FE AE FE AE FE AE FE E FE AE HEHE HERE EEE H First random loops are added into the core structures i e packed SSE backbones with side ch
9. Location Location of the input ensemble directory outPackedStructures Name of the output packed structure only the common name of all structures in the enemble For exameple the name H2H1New will generate an ensemble of structures with file names H2H1Newl pdb H2H1New3 pdb H2H1New3 pdb etc resolCluster Resolution used in the clustering step 20 7 Examples Two examples including tests on ubiquitin and FF2 structures come with the distribution of RDC PANDA version 1 0 The input data parameter files and shell scripts for running these two examples can be found in sub directory experiments The details on running RDC ANALYTIC on these two proteins can be found in the RDC ANALYTIC manual Section 6 page 9 To run these two examples namely testing RDC PANDA on proteins ubiquitin and FF2 first clear the following directory and make them empty inputFiles Jxplor local min Jxplor final cal and then type chmod 700 test NAME Jtest NAME in which NAME can be ff2 ubq and eta for each testing case For example to test RdcPanda on ubq protein type chmod 700 test ubq nohup test_ubq The locations of intermediate results can be found in remark sections of the shell scripts It is recommended that different testing cases should run in different RDC PANDA working directories The following gives an example of the shell scripts for running the ubiquitin test Shell Script File test_ubq
10. RDC PANDA User Manual Version 1 0 Jianyang Michael Zeng and Bruce R Donald Copyright O 2001 2010 Bruce Donald Lab Duke University Contents I ug te MEM HT 3 PA License ruris TIRE T E a er ene 6 a Citation E OT E 7 EMI CHE ire EON TTL 7 5 System Cofi s rati Sese secorre rE rE EE EE EE E EEE E EEEE TAS EErEE TESS 9 6 RDC PANDA Commands RP ERER 11 ps cung p EER 2 B RDC PANDA CI2388 Summary iiie esencia p eo api tial hcec i emi a es Do pi ca eee DU IE ON Co n ad eub Uie 26 1 Introduction RDC PANDA RDC based SSE PAcking with NOEs for Structure Determination and NOE Assignment is a suite of programs for nuclear Overhauser effect NOE assignment and high resolution structure determination starting with a global fold calculated from exact solutions to the residual dipolar coupling RDC equations RDC PANDA is developed in the lab of Prof Bruce Donald at Duke University This user manual is for version 1 0 of the software RDC PANDA is free software and can be redistributed and or modified under the terms of the GNU Lesser General Public License as published by the Free Software Foundation either version 3 of the License or optionally any later version RDC PANDA is distributed in the hope that it will be useful but WITHOUT ANY WARRANTY without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE
11. ReadPDBEnergy ReadNoeEnergy input This command reads the energy values from Xplor PDB files and output the top structures with lowest energies A typical input parameter file includes the following parameters LocationSSEEnsemble Location of the input Xplor PDB ensemble IsCutOff Whehter a cutoff is used for selecting top ensemble of structure Cutoff The cutoff of energy if IsCutOff is 1 OutputNumber If the cutoff is not used the top number of structures with lowest energies rowPos colPos Position of energy terms in the REMARK section of Xplor PDB files starting from 0 isOutput Whether the same PDB with the remark is outputted OutName File name of output PDBs CheckNoeByEnsemble CheckNoeByEnsemble input This command uses the voting scheme to obtain the consensus NOE assignments which are consistent with a majority of the structure in the ensemble A typical input parameter file includes the following parameters Sequence File name of protein primary sequence InputPdbLocation Location of the input ensemble of PDBs used for pruning NOE assignments PdbNameScheme Atom naming scheme of backbone PDB It can be BMRB OLD BMRB NEW PDB NEW or PDB OLD NOEFormat Format of source NOE table It can be XPLOR format or CYANA format NoeAtomNamingScheme Atom naming scheme in the NOE table InputNoeTable File name of the input NOE table isMultiAssignment Whether th
12. ains using the following commands java cp bin RdcPanda addRandomLoops addRandomLoops input gt addRandomLoops out The ensemble of complete structures with random loops will be ouputted in directory xplor local min structure which will be used as initial templates for the local minimization approach in Xplor Then go to the directory xplor local min and run the following three Xplor scripts for the local minimization cd SPWD xplor local min xplor min inp min out 22 Sxplor dgsa inp gt dgsa out xplor refine inp gt refine out Ensemble of final complete structures both SSEs and loops after the local fminimization approach will be stored in xplor local min final 5 1 Use following Xplor NIH script to evaluate the well packed structures WPSs Sxplor py calEnergy py gt computeWPS out compute average structures for ensemble of packed structures computed by PACKER the average structure will be store in xplor local_min average_all pdb Sxplor lt average_all inp gt average_all out compute average structures for ensemble of well packed structures the average structure will be store in xplor local_min average_wps pdb Sxplor lt average_wps inp gt average_wps out FE HE TE FE HE HEH EE EH EH HE FE HERE FE HE TE FE E TE RE TE ER ER ER HE HE EE E E E E E E EE BE EE HE 6 Compute the long loop in residues 50 65 FE HE TE FE FE HE FE FE HE TE FE E TE FE HE
13. al_cal 23 cp av ubiquitin noe loopsl1 0 tbl ubiquitin noe loopsl tbl cp av ubiquitin noe loops2 0 tbl ubiquitin noe loops2 tbl fempty intermediate directories rm rf pdb rm rf accept rm rf top Sxplor lt ubq loops fix inp gt compute long loops 1 out cp av pdb top TES4SASASATEAEATSTET iteration 2 for computing long loops cd cd refine those unique NOE assignments in long loop regions other NOEs are unchanged java cp bin RdcPanda CheckNoeByEnsemb CheckNoeByEnsemble loopsl input gt checkLoopNoeByEnsemble 1l out java cp bin RdcPanda CheckNoeByEnsemb CheckNoeByEnsemble loops2 input checkLoopNoeByEnsemble 2 out cd SPWD xplor final cal fempty intermediate directories rm rf pdb rm rf accept rm rf top Sxplor ubq loops fix inp gt compute long loops 2 out move all 10 structures to xplor final cal top cp av pdb top compute the inital structure template for final structure calculation Sxplor average top fix inp gt average top fix2 out Go to RdcPanda working directory ed cd HEHEHE HH HH HH HEHE HE HEH iteration 3 for computing long loops java cp bin RdcPanda HANA NOE Asg HANA NOE Asg fix input gt HANA NOE ASG fix out cd SPWD xplor final cal cp av ubiquitin noe tbl ubiquitin noe 0 tbl empty intermediate direct
14. b Bruce Donald EE Eu X O OXP Duke University XX kK qp RDCs Department of Computer Science EK 1 7 Levine Science Research Center LSRC ZS RK pa Durham SS Ce ail el erg o NC 27708 0129 USA K CAM LC CI ud kk kk k k kk E J Zeng J Boyles C Tripathy L Wang A Yan P Zhou and B R Donald ui RON High Resolution Protein Structure Determination Starting with a Global AX RU Fold Calculated from Exact Solutions to the RDC Equations J Biom NMR ae SH 45 3 265 281 2009 FE Ck Ck ck ck kk ck Ck ck Ck kk Ck Sk ck Ck Sk ck Ck ck KK KK KKK KKK KKK ck kk KK KKK ck Ck ck ck kk KKK KKK ck kk Ck ck ck kk ck kk ck kk ko kk Ck kk ko kk kk ck ko ko KK KKK KK RDC PANDA Once the program is started the desired functions can be executed through the command line The details of commands and corresponding parameter files will be described next The templates of command lines can be found in doc command template txt The structure determination through RDC Panda is generally divided into steps 1 RDC ANALYTIC is used to compute the SSE backbones from RDCs 2 PACKER is invoked to pack SSEs 3 HANA is used to compute the rotamers based on NOE pattern matching technique The loops are computed through the local minimization approach The NOE assignments are computed by HANA 4 Xplor is called to calculate the structures based on the NOE assignment table computed by HANA How to compile the progra
15. bin sh HHEHHHHEEHEEEESESE EHH TESTSTAXHETAXHSESETXSHEEOAHSHERAHAHUHES EHE 1 initialization AE AE aE aE aT aE aE aE FE aE aE HE aE aE aE aE aE aE HE EE FE FE AE AE AE AE AE aE AE AE AE aE FE aE E AE aE aE aE aE HE aE aE aE 1 1 set the XPLOR NIH path xplor usr project dlab Users Software xplor NIH 64 xplor nih 2 16 0 bin xplor 1 2 Empty the inputfile directory dto be safe it would be better to empty these directories manually rm rf SPWD inputFiles rm rf SPWD xplor 1 3 Copy the input files from experiments directory 21 cp av PWD experiments ubq inputFiles SPWD inputFiles 1 4 Copy the Xplor scripts to the Xplor working directory cp av SPWD experiments ubq xplor SPWD xplor FE FEE HE E REE E FEAE EE RHEE FE FE RHEE EEE RHEE EEE EERE EEE HERE EEE HERE EEF 2 Run RDC Analytic program to compute the SSE backbones from RDCs HEHE HEHEHE HE FE HE HEHE FE FE FE FE FE EEE FE FE EE EEA E FE E FE E TE HEE EEE HEE EEF go to RDC ANALYTIC directory and compute SSE backbones cd RdcAnalytic java analytic RDCAnalytic RDC ANALYTIC out copy the PDB files from RDC ANALYTIC to the RDC PANDA input file directory cp av helixl pdb RdcPanda inputFiles cp av sheetl pdb RdcPanda inputFiles go to RDC PANDA directory cd RdcPanda FE HE TE FE E TE FE FE HE FE FE EH EH EH HH FE AE EEE EE E
16. bond vectors 5 the TALOS table of dihedral angle ranges from the chemical shift analysis optional 6 the rotamer library RDC PANDA has been used to solve the new structures of the FF Domain 2 of human transcription elongation factor CA150 RNA polymerase II C terminal domain interacting protein FF2 The new NMR structures have been deposited into Protein Data Bank PDB ID 2KIQ Stage 1 CH amp NH RDCs RDC ANALYTIC C C amp NC RDCs optional Orientations amp conformations of SSE backbones Packing algorithm PACKER Resonance assignments JP jal NOESY peak list Packed SSE backbones core structure HANA b e NOESY peak list Rotamer library 39 Side chain placement L BONS assignments Initial NOE assignment Lu Core structure with side chains Filtration of ambiguous NOE assignments i Unambiguous NOE restraints i Local minimization approach fixing core structure as a rigid body Low resolution structure Filtration of ambiguous NOE assignments Ambiguous NOE assignments NOESY peak list Resonance assignments NOE assignments XPLOR XPLOR NIH Calculated structures Prune violated NOE assignments Refined NOE assignments XPLOR XPLOR NIH High resolution structures Figure 1 Flow chart of RDC P
17. e following parameters Sequence File name of protein primary sequence chFile File name of CH RDCs nhFile File name of NH RDCs cocaFile File name of CaC RDCs This parameter is set to be null if CaC RDCs are not available conFile File name of NC RDCs This parameter is set to be null if NC RDCs are not available WtCoCA wtCoN Weighting factor between CH NH RDCs and CaC and NC RDCs in the scoring function used in systematic search for computing the dihedral angle solutions Syy Szz Diagonal elements of Saupe order matrix of alignment tensor SseBoundaries Residue boundaries for all beta strands The start and end residues should be separated by 5 PrePdbName The PDB file name of previous backbone fragment This is used for computing a long helix when the helix is divided into two parts This parameter is set to be null for computing a single fragment hBonds File name of hydrogen bonds used for packing bete strands OutPdbName File name of output PDB file name of computed backbone TALOS File name of the TALOS angle table This command is not longer under the maintenance This updated version of this function can be found in the latest version of RDC ANALYTIC SSEPacking packingSSEs input This command line packs SSEs using the PACKER algorithm A typical input parameter file includes the following parameters Sequence File name of protein primary sequence
18. e input checkNoeByEnsemble_2 out cd SPWD xplor final_cal fempty intermediate directories ri EE pdb rm rf accept tm rf top sxplor lt ubgq l inp gt final call ont Go to RdcPanda workding directory cd cd move all 10 structures to xplor final cal top java cp bin RdcPanda ReadPDBEnergy ReadNoeEnergy input ReadEnergy final 2 out cd SPWD xplor final cal Sxplor average top 2 inp gt average top 2 out Go to RdcPanda workding directory cd ca 8 RDC PANDA Class Summary This section provides a summary of the RDC PANDA classes which will be useful for users to modify and extend the RDC PANDA source code More details about the definitions of the RDC PANDA classes and methods in the java source code can be found in sub directory doc javadoc in html format e Assign This class provides functions that involve NOE assignment such as initial NOE assignment using only chemical shift information and prune ambiguous NOE assignments using given the structural information etc e BackNoe This class provides functions that involve back computed NOEs e Cartesian This class defines Cartesian coordinates for individual atom in protein structure e Const This class defines various global constants for the entire program 26 Dipolar This class provides data structures processing experimental RDC data EigenvalueDecomposition This class is extended from t
19. e input NOE table is in the multiple assignment format noeLimit Upper limit for pruning ambiguous NOEs When it is negative the original upper bound calibrated from peak intensity is used NoeCutOff Percentage threshold of the structures in the ensemble for checking the consistency of NOE assignments Suppose the NoeCutOff is 0 6 If more than 60 of structures in the ensemble are consistent with an NOE assignment this NOE assignment is outputted Otherwise it is pruned OutNOETable File name of new NOE table after deleting those violated NOEs isOutVioNOEs Whether those violated NOEs are outputted as the remarks isOutMultiAsgFormat Whether new NOE assignments are outputted in the multiple NOE Assignment format NoeStatistics NoeStatistics input This command gives the statistical summary of an NOE assignment table A typical input parameter file includes the following parameters Sequence File name of protein primary sequence NOEFormat Format of source NOE table It can be XPLOR format or CYANA format NoeAtomNamingScheme Atom naming scheme in the NOE table InputNoeTable File name of the input NOE table isMultiAssignment Whether the input NOE table is in the multiple assignment format mergeNClusterAll mergeNClusterAll input This command performs the clustering step over all packed structures in a single directory A typical input parameter file includes the following parameters InputFile
20. factor between CH NH RDCs and CaC and NC RDCs in the scoring function used in systematic search for computing the dihedral angle solutions Syy Szz Diagonal elements of Saupe order matrix of alignment tensor ResBounds Residue boundaries of the helix The start and end residues should be separated by PrePdbName The PDB file name of previous backbone fragment This is used for computing a long helix when the helix is divided into two parts This parameter is set to be null for computing a single fragment OutPdbName File name of output PDB file name of computed backbone TALOS File name of the TALOS angle table This command is not longer under the maintenance This updated version of this function can be found in the latest version of RDC ANALYTIC RdcExactHelixWOAT RdcExactHelixWOAT input This command line computes the helix backbone without requiring the alignment tensor information The input parameter file is similar to RdcExactHelix input except the inputs of diagonal elements of Saupe matrix are not required This command is not longer under the maintenance This updated version of this function can be found in the latest version of RDC ANALYTIC RdcExactSheet RdcExactSheet input This command is used to compute the beta sheet backbone from RDCs using the RDC EXACT algorithm CH and NH RDCs are required as input files while CaC and NC RDCs are optional A typical input parameter file includes th
21. he Jama package which provides the methods for the eigenvalue decomposition of a matrix HICS This class provides data structures that involve chemical shifts Hbond This class defines data structures related to h bonds Hdist This class provides data structures related to back computed NOE distance restraints IDof2aryStructure This class provides functions for processing files with secondary structure element information Maths This class is modified from the Jama numeric package which provides some math operations that are used in the program Matrix This class is modified from the Jama numeric package which provides some matrix operations that are used in the program Model This class provides functions that compute backbone from RDC EXACT algorithm ModelRdc This class provides methods for computing all the backbone dihedral phi psi angles of an alpha helix or a beta strand based on exact solution and a systematic search Noe This class provides data structures and functions for processing NOE assignment Noesy This class provides data structures and functions for processing NOESY spectra Pdb This class provides data structures and functions for processing and generating PDB files and extracting backbone angles etc PdbRdc This class provides various SVD methods for best fitting RDCs and a structural fragment and grid search method for computing the three Euler angles PhiPsi This class provides various method
22. information It then applies a 3D grid search to find all discrete translations that satisfy the sparse NOE distance restraints When packing each pair of SSE backbones all four fold symmetries of SSE orientations are also taken into account 3 HANA HAusdorff based NOE Assignment which uses the SSE backbones to place side chains and assign NOEs HANA first computes a set of initial NOE assignments by considering all pairs of protons that are possibly assigned to an NOE cross peak if the resonances of corresponding atoms fall within a tolerance window Then a Hausdorff based pattern matching technique is employed to deduce similarity between experimental and back computed NOE spectra for each rotamer from a statistically diverse library and drive the selection of optimal position specific rotamers for filtering ambiguous NOE assignments In addition to above three modules a local minimization approach is used to compute loops and refine side chain conformations by fixing the core structure as a rigid body while allowing movement of loops and side chains Figure 1 shows the flow chart of RDC PANDA The input data to RDC PANDA include 1 the primary sequence of the protein 2 the 3D NOE peak list from both 15N and 13C edited spectra 3 the resonance assignment list including both backbone and side chain resonance assignments 4 the RDC data including CH and NH RDCs and the RDCs of other bond vectors optional such as CA C and NC
23. le of an input parameter file ceading protein sequence sequence UBQ seq format of resonance assignments CYANA for the CYANA format BMRB for BMRB format XEASY for XEASY format resFormat CYANA atome naming scheme in the resonance list resNameScheme BMRB NEW eg HB1 HB2 for GLU etc name of resonance assignment file resonance ubc cyana prot convert txt 10 reading NOESY peak lists 3D N15 NOESY ubc n15 noe peaks 3D C13 NOESY ubc_c13_noe peaks All input parameter files are stored in directory inputFiles System Files All system files of RDC PANDA are stored in sub directory system This sub directory includes the rotamer library system parameters e g location of the input files and BMRB statistical information 6 RDC PANDA Commands RdcExactHelix RdcExactHelix input This command computes the helix backbone from RDCs using the RDC EXACT algorithm CH and NH RDC Ss are required as input files while CaC and NC RDCs are optional A typical input parameter file includes the following parameters Sequence File name of protein primary sequence chFile File name of CH RDCs nhFile File name of NH RDCs cocaFile File name of CaC RDCs This parameter is set to be null if CaC RDCs are not available conFile File name of NC RDCs This parameter is set to be null if NC RDCs are not available wtCoCA wtCoN Weighting
24. m optional 1 Install Java Development Kit JDK The newest version of JRE can be downloaded from http java sun com javase downloads 2 Modify the Makefile under the RDC PANDA working directory as needed In particular specify your working directory and the paths to your Java compiler and resources 3 Under the RDC PANDA working directory type make 5 System Configurations File Organization The directory structure of RDC PANDA is organized as follows Jexperiments This directory contains data and input parameter files used for the experiments with proteins FF2 and ubiquitin Jbin This directory contains the java executable files src This directory contains the java source codes inputFiles This directory contains input data and parameter files JoutputFiles This directory is used as the location where output files are written to Jdoc This directory contains the documentations of the program system This directory contains the system configuration files The directory path of input data and parameter files can be set in system system parameters txt Jxplor This directory is used for running Xplor scripts and storing corresponding results Required NMR Data and Formats RDCs CH and NH RDCs are required Other RDCs such as CaC and NC RDCs are optional Format residue index RDC value unscaled experimental error 0 0 In RDC ANALYTIC RDCs are in standard Xplor format Resona
25. nce assignments The resonance assignment list should contain both backbone and side chain resonance assignments Format XEASY format CYANA format or BMRB deposition format Sequence The primary sequence of the protein Format residue name residue index NOESY cross peaks 3D or 4D DN or PC edited NOESY peak list Format XEASY format or NMRVIEW format TALOS dihedral angle restraints Optional The TALOS table provides interval restraints of dihedral angles estimated from chemical chemical shift analysis Format residue index residue name Phi or Psi average value error bar Atom Naming Schemes In RDC Panda the following four atom naming schemes in the input files are supported PDB NEW eg HA1 HA2 Gly PDB OLD eg 1HA 2HA Gly BMRB NEW eg HA2 HA3 Gly BMRB OLD eg 2HA 3HA Gly In the program all atom names are first converted to the PDB NEW naming scheme Input Parameter File Format This section describes the different commands and the corresponding required parameters Each command line consists of command and the file name of input parameter file The command and the parameter file name must be separated by space In the input parameter file lines starting with are parsed as comments Parameter names are single words parameter values follow the corresponding parameter name on the same line and are separated by Each parameter line ends with the symbol The following gives an examp
26. ngs In Proceedings of the 2004 IEEE Computational Systems Bioinformatics Conference CSB 04 Stanford CA pages 319 330 2004 4 Installation System Requirements To use this software Java Runtime Environment from Sun Microsystems JRE must be installed The newest version of JRE can be downloaded from http java sun com javase downloads How to install the program 1 Install Java Runtime Environment from Sun Microsystems JRE The newest version of JRE can be downloaded from http java sun com javase downloads 2 Create a working directory Use gunzip and tar commands to decompress Rdc Analytic_Panda_V1 0_Jan_2010 tgz and extract all files in the working directory 3 Install Xplor Xplor NIH The newest version of Xplor Xplor NIH can be download from http nmr cit nih gov xplor nih How to run the program To run the RDC Panda software go to the RDC PANDA working directory which contains the bin sub directory and use the following command java cp bin RdcPanda Or alternatively use the following commands chmod 755 RdcPanda RdcPanda If the program runs successfully the following txt interface should be given Ck ck ck ck ck ck Ck ck ck kk Ck Sk ck Ck ck Ck ck Ck KKK KKK KKK ck Ck ck ck ck KKK KKK KKK KK KKK KKK KKK ck kk ck kk Ck kk kk ck kk Sk kk ck kk Sk kc k ko kc kc kckockokok ax rMr rMr RDC PANDA Version 1 0 EK XE CND 2ND Contact Info ae EK P xMx yM
27. ntact Info Bruce R Donald Duke University Department of Computer Science Levine Science Research Center LSRC Durham NC 27708 0129 USA e mail www cs duke edu brd signature of Bruce Donald 01 December 2009 Bruce R Donald Professor of Computer Science and Biochemistry 3 Citation Requirements You are required to cite our papers in any publications that use this code The primary citation corresponding to this software is 1 The papers that can be cited based on or related to this software are listed below 1 Jianyang Zeng Jeffrey Boyles Chittaranjan Tripathy Lincong Wang Anthony Yan Pei Zhou and Bruce Randall Donald High resolution protein structure determination starting with a global fold calculated from exact solutions to the RDC equations Journal of Biomolecular NMR 45 3 265 281 2009 2 Bruce R Donald and Jeffrey Martin Automated NMR Assignment and Protein Structure Determination using Sparse Dipolar Coupling Constraints Progress in Nuclear Magnetic Resonance Spectroscopy 55 2 101 127 2009 3 Lincong Wang Ramgopal R Mettu and Bruce R Donald A Polynomial Time Algorithm for De Novo Protein Backbone Structure Determination from NMR Data Journal of Computational Biology 13 7 1276 1288 2006 4 Lincong Wang and Bruce Randall Donald Analysis of a Systematic Search Based Algorithm for Determining Protein Backbone Structure from a Minimal Number of Residual Dipolar Coupli
28. ories rm rf pdb 24 rm rf accept rm rf top Sxplor lt ubg loops fix2 inp gt compute long loops 3 out move all 10 structures to xplor final cal top cp av pdb top compute the inital structure template for final structure calculation xplor average top fix inp average top fix3 out Go to RdcPanda workding directory cd cd TRE UEERERHHEUEREREREREREREREREREREUEERERRUEHERETSSSERdHESESESAHSTETIHTETSSA3HEAqdHHSHSH 7 Final structure calculation FEAE AE aE AE AE aE aE E FE aE AE AE AE E aE aE AE HE a HE aE HE aa aa E E aaa aE aaa HEE aaa FE FE H HEHEHE HEH EH EH ERE ERE ERE E E Round 1 Use HANA to compute the NOE assignments java cp bin RdcPanda DANA NOE Asg HANA NOE Asg fix input gt DANA NOE ASG 1l out cd SPWD xplor final cal cp av ubiquitin noe tbl ubiquitin noe 0 tbl fempty intermediate directories rm rf pdb rm rf accept rm rf top 9xplor lt ubq l inp gt final cal 1 0 Ut Go to RdcPanda workding directory cd ca move all 10 structures to xplor final cal top java cp bin RdcPanda ReadPDBEnergy ReadNoeEnergy input gt ReadEnergy final 1 out cd SPWD xplor final cal Sxplor lt average top l inp gt average top 1l out Go to RdcPanda workding directory cd ca TEXAS UEHERE RE RE HERE ERE RE ERE EHF Round 2 25 java cp bin RdcPanda CheckNoeByEnsemble CheckNoeByEnsembl
29. ructure after combining side chains and backbone are used as the NOE upper bounds IsCheck Whether checking the NOE assignment results by comparing them with the reference structure refPdb File name of the reference structure PDB when ischeck is 1 refNameScheme Atom naming scheme for the reference structure It can be BMRB OLD BMRB NEW PDB NEW or PDB OLD CalAlignmentTensor calAlignmentTensor input This command computes the alignment tensor given CH and NH RDCs and PDB Although CaC and NC RDCs can be inputted into the program only CH and NH RDCs are used for computing alignment tensor However the RMSD values between experimental and back computed RDCs for CaC NC CH and NH RDCs are all reported A typical input parameter file includes the following parameters 16 chFile File name of CH RDCs nhFile File name of NH RDCs cocaFile File name of CaC RDCs This parameter is set to be null if CaC RDCs are not available conFile File name of NC RDCs This parameter is set to be null if NC RDCs are not available InputPdbName File name of input PDB NOEAsgFromCS asg noe cs input This command assigns NOEs based on only chemical shift information A typical input parameter file includes the following parameters Sequence File name of protein primary sequence haErr Klee Gl3Err hnErr AETI Error windows in each dimension ppm
30. s for exact solution and systematic search including the computation of rotation to the first peptide plane the DFS search and solver of the quartic equation and the computation phi and psi angles from two vectors in consecutive planes etc Rotamer This class provides data structures and functions related to rotamers RotaPattern This class implements data structures and functions that deal with the rotamer properties such as NOE pattern for each rotamer 27 SingularValueDecomposition This class provides functions for SVD operations from Jama package SSEPacking This class provides functions for packing SSE fragments vdw This class provides methods for computing the vdw energy term 28
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